Starting phenix.real_space_refine on Fri Aug 22 12:37:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b3a_15824/08_2025/8b3a_15824.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b3a_15824/08_2025/8b3a_15824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b3a_15824/08_2025/8b3a_15824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b3a_15824/08_2025/8b3a_15824.map" model { file = "/net/cci-nas-00/data/ceres_data/8b3a_15824/08_2025/8b3a_15824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b3a_15824/08_2025/8b3a_15824.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1320 2.51 5 N 450 2.21 5 O 240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2010 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.45, per 1000 atoms: 0.22 Number of scatterers: 2010 At special positions: 0 Unit cell: (90.48, 49.92, 37.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 240 8.00 N 450 7.00 C 1320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=30, symmetry=0 Number of additional bonds: simple=30, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 66.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 420 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 47.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 removed outlier: 6.335A pdb=" N LEU A 3 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU G 3 " --> pdb=" O HIS M 4 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU M 3 " --> pdb=" O HIS S 4 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU S 3 " --> pdb=" O HIS Y 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 4 removed outlier: 6.335A pdb=" N LEU B 3 " --> pdb=" O HIS H 4 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU H 3 " --> pdb=" O HIS N 4 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU N 3 " --> pdb=" O HIS T 4 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU T 3 " --> pdb=" O HIS Z 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 6 removed outlier: 6.270A pdb=" N LEU C 3 " --> pdb=" O HIS I 4 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ARG I 6 " --> pdb=" O LEU C 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU C 5 " --> pdb=" O ARG I 6 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU I 3 " --> pdb=" O HIS O 4 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ARG O 6 " --> pdb=" O LEU I 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU I 5 " --> pdb=" O ARG O 6 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU O 3 " --> pdb=" O HIS U 4 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ARG U 6 " --> pdb=" O LEU O 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU O 5 " --> pdb=" O ARG U 6 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU U 3 " --> pdb=" O HIS a 4 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ARG a 6 " --> pdb=" O LEU U 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU U 5 " --> pdb=" O ARG a 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 2 through 6 removed outlier: 6.270A pdb=" N LEU D 3 " --> pdb=" O HIS J 4 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ARG J 6 " --> pdb=" O LEU D 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU D 5 " --> pdb=" O ARG J 6 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU J 3 " --> pdb=" O HIS P 4 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ARG P 6 " --> pdb=" O LEU J 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU J 5 " --> pdb=" O ARG P 6 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU P 3 " --> pdb=" O HIS V 4 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ARG V 6 " --> pdb=" O LEU P 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU P 5 " --> pdb=" O ARG V 6 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU V 3 " --> pdb=" O HIS b 4 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ARG b 6 " --> pdb=" O LEU V 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU V 5 " --> pdb=" O ARG b 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 2 through 6 removed outlier: 6.372A pdb=" N LEU E 3 " --> pdb=" O HIS K 4 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ARG K 6 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU E 5 " --> pdb=" O ARG K 6 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU K 3 " --> pdb=" O HIS Q 4 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ARG Q 6 " --> pdb=" O LEU K 3 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU K 5 " --> pdb=" O ARG Q 6 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU Q 3 " --> pdb=" O HIS W 4 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ARG W 6 " --> pdb=" O LEU Q 3 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU Q 5 " --> pdb=" O ARG W 6 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU W 3 " --> pdb=" O HIS c 4 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ARG c 6 " --> pdb=" O LEU W 3 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU W 5 " --> pdb=" O ARG c 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 2 through 6 removed outlier: 6.372A pdb=" N LEU F 3 " --> pdb=" O HIS L 4 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ARG L 6 " --> pdb=" O LEU F 3 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU F 5 " --> pdb=" O ARG L 6 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU L 3 " --> pdb=" O HIS R 4 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ARG R 6 " --> pdb=" O LEU L 3 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU L 5 " --> pdb=" O ARG R 6 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU R 3 " --> pdb=" O HIS X 4 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ARG X 6 " --> pdb=" O LEU R 3 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU R 5 " --> pdb=" O ARG X 6 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU X 3 " --> pdb=" O HIS d 4 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ARG d 6 " --> pdb=" O LEU X 3 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU X 5 " --> pdb=" O ARG d 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.03 Time building geometry restraints manager: 0.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.27: 240 1.27 - 1.34: 420 1.34 - 1.41: 180 1.41 - 1.47: 240 1.47 - 1.54: 930 Bond restraints: 2010 Sorted by residual: bond pdb=" C HIS I 4 " pdb=" N LEU I 5 " ideal model delta sigma weight residual 1.331 1.278 0.053 1.55e-02 4.16e+03 1.16e+01 bond pdb=" C HIS U 4 " pdb=" N LEU U 5 " ideal model delta sigma weight residual 1.331 1.278 0.053 1.55e-02 4.16e+03 1.15e+01 bond pdb=" C HIS a 4 " pdb=" N LEU a 5 " ideal model delta sigma weight residual 1.331 1.279 0.052 1.55e-02 4.16e+03 1.15e+01 bond pdb=" C HIS L 4 " pdb=" N LEU L 5 " ideal model delta sigma weight residual 1.331 1.279 0.052 1.55e-02 4.16e+03 1.15e+01 bond pdb=" C HIS J 4 " pdb=" N LEU J 5 " ideal model delta sigma weight residual 1.331 1.279 0.052 1.55e-02 4.16e+03 1.14e+01 ... (remaining 2005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 2018 1.52 - 3.03: 322 3.03 - 4.55: 182 4.55 - 6.07: 88 6.07 - 7.59: 60 Bond angle restraints: 2670 Sorted by residual: angle pdb=" N LEU N 3 " pdb=" CA LEU N 3 " pdb=" C LEU N 3 " ideal model delta sigma weight residual 108.96 102.19 6.77 1.59e+00 3.96e-01 1.81e+01 angle pdb=" N LEU M 3 " pdb=" CA LEU M 3 " pdb=" C LEU M 3 " ideal model delta sigma weight residual 108.96 102.19 6.77 1.59e+00 3.96e-01 1.81e+01 angle pdb=" N LEU Y 3 " pdb=" CA LEU Y 3 " pdb=" C LEU Y 3 " ideal model delta sigma weight residual 108.96 102.20 6.76 1.59e+00 3.96e-01 1.81e+01 angle pdb=" N LEU G 3 " pdb=" CA LEU G 3 " pdb=" C LEU G 3 " ideal model delta sigma weight residual 108.96 102.20 6.76 1.59e+00 3.96e-01 1.81e+01 angle pdb=" N LEU S 3 " pdb=" CA LEU S 3 " pdb=" C LEU S 3 " ideal model delta sigma weight residual 108.96 102.20 6.76 1.59e+00 3.96e-01 1.81e+01 ... (remaining 2665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.64: 860 18.64 - 37.29: 220 37.29 - 55.93: 60 55.93 - 74.57: 0 74.57 - 93.22: 30 Dihedral angle restraints: 1170 sinusoidal: 570 harmonic: 600 Sorted by residual: dihedral pdb=" CH3 ACE W 0 " pdb=" C ACE W 0 " pdb=" N LEU W 1 " pdb=" CA LEU W 1 " ideal model delta sinusoidal sigma weight residual -180.00 -86.78 -93.22 1 5.00e+00 4.00e-02 4.06e+02 dihedral pdb=" CH3 ACE K 0 " pdb=" C ACE K 0 " pdb=" N LEU K 1 " pdb=" CA LEU K 1 " ideal model delta sinusoidal sigma weight residual -180.00 -86.80 -93.20 1 5.00e+00 4.00e-02 4.05e+02 dihedral pdb=" CH3 ACE c 0 " pdb=" C ACE c 0 " pdb=" N LEU c 1 " pdb=" CA LEU c 1 " ideal model delta sinusoidal sigma weight residual -180.00 -86.82 -93.18 1 5.00e+00 4.00e-02 4.05e+02 ... (remaining 1167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 170 0.041 - 0.082: 40 0.082 - 0.123: 30 0.123 - 0.164: 17 0.164 - 0.205: 73 Chirality restraints: 330 Sorted by residual: chirality pdb=" CA HIS V 4 " pdb=" N HIS V 4 " pdb=" C HIS V 4 " pdb=" CB HIS V 4 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA HIS F 4 " pdb=" N HIS F 4 " pdb=" C HIS F 4 " pdb=" CB HIS F 4 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA HIS U 4 " pdb=" N HIS U 4 " pdb=" C HIS U 4 " pdb=" CB HIS U 4 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 327 not shown) Planarity restraints: 300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ACE J 0 " 0.089 2.00e-02 2.50e+03 3.14e-01 1.23e+03 pdb=" O ACE J 0 " -0.104 2.00e-02 2.50e+03 pdb=" CH3 ACE J 0 " -0.175 2.00e-02 2.50e+03 pdb=" N LEU J 1 " 0.556 2.00e-02 2.50e+03 pdb=" CA LEU J 1 " -0.366 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE V 0 " 0.089 2.00e-02 2.50e+03 3.14e-01 1.23e+03 pdb=" O ACE V 0 " -0.104 2.00e-02 2.50e+03 pdb=" CH3 ACE V 0 " -0.175 2.00e-02 2.50e+03 pdb=" N LEU V 1 " 0.556 2.00e-02 2.50e+03 pdb=" CA LEU V 1 " -0.366 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE P 0 " 0.089 2.00e-02 2.50e+03 3.14e-01 1.23e+03 pdb=" O ACE P 0 " -0.104 2.00e-02 2.50e+03 pdb=" CH3 ACE P 0 " -0.175 2.00e-02 2.50e+03 pdb=" N LEU P 1 " 0.556 2.00e-02 2.50e+03 pdb=" CA LEU P 1 " -0.366 2.00e-02 2.50e+03 ... (remaining 297 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 758 3.07 - 3.53: 2022 3.53 - 3.99: 2661 3.99 - 4.44: 3385 4.44 - 4.90: 6093 Nonbonded interactions: 14919 Sorted by model distance: nonbonded pdb=" N LEU Y 5 " pdb=" O LEU Y 5 " model vdw 2.613 2.496 nonbonded pdb=" N LEU A 5 " pdb=" O LEU A 5 " model vdw 2.614 2.496 nonbonded pdb=" N LEU B 5 " pdb=" O LEU B 5 " model vdw 2.614 2.496 nonbonded pdb=" N LEU Z 5 " pdb=" O LEU Z 5 " model vdw 2.614 2.496 nonbonded pdb=" N LEU M 5 " pdb=" O LEU M 5 " model vdw 2.614 2.496 ... (remaining 14914 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.120 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.102 2040 Z= 1.379 Angle : 1.900 7.587 2670 Z= 1.076 Chirality : 0.104 0.205 330 Planarity : 0.098 0.314 300 Dihedral : 27.060 93.216 750 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 42.86 % Favored : 57.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.71 (0.30), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.23), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG c 6 HIS 0.002 0.001 HIS G 2 Details of bonding type rmsd covalent geometry : bond 0.00956 ( 2010) covalent geometry : angle 1.89975 ( 2670) Misc. bond : bond 0.10093 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.044 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.2379 time to fit residues: 0.5592 Evaluate side-chains 0 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.5980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.082966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.067031 restraints weight = 7424.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.068285 restraints weight = 5035.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.069310 restraints weight = 3793.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.069953 restraints weight = 3041.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.070481 restraints weight = 2628.963| |-----------------------------------------------------------------------------| r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4986 moved from start: 1.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.259 2040 Z= 4.101 Angle : 5.842 33.338 2670 Z= 2.796 Chirality : 0.401 1.292 330 Planarity : 0.054 0.182 300 Dihedral : 12.031 32.166 270 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 288.18 Ramachandran Plot: Outliers : 42.00 % Allowed : 48.67 % Favored : 9.33 % Rotamer: Outliers : 40.00 % Allowed : 17.14 % Favored : 42.86 % Cbeta Deviations : 10.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -10.66 (0.09), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.12 (0.07), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG O 6 HIS 0.052 0.013 HIS O 4 Details of bonding type rmsd covalent geometry : bond 0.08113 ( 2010) covalent geometry : angle 5.84224 ( 2670) Misc. bond : bond 0.00538 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 0 time to evaluate : 0.048 Fit side-chains revert: symmetry clash REVERT: A 1 LEU cc_start: 0.5857 (OUTLIER) cc_final: 0.5507 (pt) REVERT: A 5 LEU cc_start: 0.5745 (OUTLIER) cc_final: 0.5285 (tt) REVERT: B 1 LEU cc_start: 0.5865 (OUTLIER) cc_final: 0.5513 (pt) REVERT: B 5 LEU cc_start: 0.5774 (OUTLIER) cc_final: 0.5324 (tt) REVERT: C 5 LEU cc_start: 0.5963 (OUTLIER) cc_final: 0.5666 (tt) REVERT: D 5 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.5545 (tt) REVERT: E 5 LEU cc_start: 0.5936 (OUTLIER) cc_final: 0.5588 (tt) REVERT: F 5 LEU cc_start: 0.5964 (OUTLIER) cc_final: 0.5622 (tt) REVERT: G 5 LEU cc_start: 0.5576 (OUTLIER) cc_final: 0.5187 (tt) REVERT: H 5 LEU cc_start: 0.5549 (OUTLIER) cc_final: 0.5165 (tt) REVERT: K 5 LEU cc_start: 0.5700 (OUTLIER) cc_final: 0.5399 (tt) REVERT: L 5 LEU cc_start: 0.5694 (OUTLIER) cc_final: 0.5377 (tt) REVERT: M 5 LEU cc_start: 0.5612 (OUTLIER) cc_final: 0.5186 (tt) REVERT: N 5 LEU cc_start: 0.5678 (OUTLIER) cc_final: 0.5226 (tt) REVERT: O 4 HIS cc_start: 0.4938 (OUTLIER) cc_final: 0.4110 (m90) REVERT: O 5 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.5555 (tt) REVERT: P 4 HIS cc_start: 0.4863 (OUTLIER) cc_final: 0.4139 (m90) REVERT: Q 5 LEU cc_start: 0.5870 (OUTLIER) cc_final: 0.5500 (tt) REVERT: R 5 LEU cc_start: 0.5805 (OUTLIER) cc_final: 0.5445 (tt) REVERT: W 5 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.6066 (tt) REVERT: X 5 LEU cc_start: 0.6135 (OUTLIER) cc_final: 0.5749 (tt) outliers start: 84 outliers final: 37 residues processed: 84 average time/residue: 0.0159 time to fit residues: 1.8070 Evaluate side-chains 58 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 0 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 4 HIS Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain Q residue 1 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 1 LEU Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain c residue 1 LEU Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain d residue 1 LEU Chi-restraints excluded: chain d residue 2 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.083789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.067404 restraints weight = 8006.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.068673 restraints weight = 5279.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.069733 restraints weight = 3935.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.070586 restraints weight = 3148.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.071388 restraints weight = 2642.757| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5605 moved from start: 1.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.273 2040 Z= 4.022 Angle : 5.698 34.006 2670 Z= 2.689 Chirality : 0.407 1.316 330 Planarity : 0.051 0.162 300 Dihedral : 11.533 31.208 270 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 282.74 Ramachandran Plot: Outliers : 36.67 % Allowed : 59.33 % Favored : 4.00 % Rotamer: Outliers : 46.67 % Allowed : 20.00 % Favored : 33.33 % Cbeta Deviations : 12.86 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -10.75 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.19 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG c 6 HIS 0.051 0.014 HIS C 4 Details of bonding type rmsd covalent geometry : bond 0.08083 ( 2010) covalent geometry : angle 5.69768 ( 2670) Misc. bond : bond 0.00553 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 0 time to evaluate : 0.050 Fit side-chains revert: symmetry clash REVERT: A 2 HIS cc_start: 0.6016 (OUTLIER) cc_final: 0.5693 (t-170) REVERT: A 5 LEU cc_start: 0.6223 (OUTLIER) cc_final: 0.5742 (tt) REVERT: B 2 HIS cc_start: 0.6027 (OUTLIER) cc_final: 0.5656 (t-170) REVERT: B 5 LEU cc_start: 0.6263 (OUTLIER) cc_final: 0.5773 (tt) REVERT: C 4 HIS cc_start: 0.5880 (OUTLIER) cc_final: 0.4966 (m90) REVERT: C 5 LEU cc_start: 0.6307 (OUTLIER) cc_final: 0.5948 (tt) REVERT: D 4 HIS cc_start: 0.6413 (OUTLIER) cc_final: 0.5319 (m90) REVERT: D 5 LEU cc_start: 0.6361 (OUTLIER) cc_final: 0.6034 (tt) REVERT: E 5 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.6231 (tt) REVERT: F 5 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6342 (tt) REVERT: G 5 LEU cc_start: 0.6384 (OUTLIER) cc_final: 0.5892 (tt) REVERT: H 5 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.5905 (tt) REVERT: I 5 LEU cc_start: 0.6245 (OUTLIER) cc_final: 0.5956 (tt) REVERT: K 5 LEU cc_start: 0.6356 (OUTLIER) cc_final: 0.6061 (tt) REVERT: L 5 LEU cc_start: 0.6300 (OUTLIER) cc_final: 0.5971 (tt) REVERT: M 5 LEU cc_start: 0.6220 (OUTLIER) cc_final: 0.5655 (tt) REVERT: N 5 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.5691 (tt) REVERT: O 2 HIS cc_start: 0.5708 (OUTLIER) cc_final: 0.5088 (t-170) REVERT: O 4 HIS cc_start: 0.6146 (OUTLIER) cc_final: 0.5050 (t70) REVERT: P 2 HIS cc_start: 0.5727 (OUTLIER) cc_final: 0.5133 (t-170) REVERT: P 4 HIS cc_start: 0.6292 (OUTLIER) cc_final: 0.5144 (t70) REVERT: P 5 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.6071 (tt) REVERT: Q 1 LEU cc_start: 0.6267 (OUTLIER) cc_final: 0.6025 (pt) REVERT: Q 5 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6166 (tt) REVERT: R 1 LEU cc_start: 0.6370 (OUTLIER) cc_final: 0.6164 (pt) REVERT: R 5 LEU cc_start: 0.6468 (OUTLIER) cc_final: 0.6018 (tt) REVERT: W 4 HIS cc_start: 0.6604 (OUTLIER) cc_final: 0.6377 (t70) REVERT: W 5 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6429 (tt) REVERT: X 4 HIS cc_start: 0.6502 (OUTLIER) cc_final: 0.6222 (t70) REVERT: X 5 LEU cc_start: 0.6468 (OUTLIER) cc_final: 0.6181 (tt) REVERT: c 5 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6894 (tt) REVERT: d 5 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6775 (tt) outliers start: 98 outliers final: 47 residues processed: 98 average time/residue: 0.0161 time to fit residues: 2.1289 Evaluate side-chains 79 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 0 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 2 HIS Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 4 HIS Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 HIS Chi-restraints excluded: chain O residue 4 HIS Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 2 HIS Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain Q residue 1 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 1 LEU Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain V residue 2 HIS Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain c residue 1 LEU Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 1 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 5 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.083591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.066849 restraints weight = 8355.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.068146 restraints weight = 5518.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.069294 restraints weight = 4122.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.070192 restraints weight = 3249.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.070890 restraints weight = 2682.310| |-----------------------------------------------------------------------------| r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4933 moved from start: 1.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.279 2040 Z= 3.999 Angle : 5.689 34.359 2670 Z= 2.701 Chirality : 0.408 1.329 330 Planarity : 0.051 0.155 300 Dihedral : 11.283 31.397 270 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 281.09 Ramachandran Plot: Outliers : 36.00 % Allowed : 60.00 % Favored : 4.00 % Rotamer: Outliers : 50.95 % Allowed : 16.67 % Favored : 32.38 % Cbeta Deviations : 13.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -10.74 (0.09), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG O 6 HIS 0.051 0.013 HIS C 4 Details of bonding type rmsd covalent geometry : bond 0.07998 ( 2010) covalent geometry : angle 5.68945 ( 2670) Misc. bond : bond 0.00550 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 0 time to evaluate : 0.050 Fit side-chains REVERT: A 5 LEU cc_start: 0.5661 (OUTLIER) cc_final: 0.5206 (tt) REVERT: B 2 HIS cc_start: 0.5565 (OUTLIER) cc_final: 0.5352 (t-170) REVERT: B 5 LEU cc_start: 0.5670 (OUTLIER) cc_final: 0.5226 (tt) REVERT: C 2 HIS cc_start: 0.5461 (OUTLIER) cc_final: 0.5054 (t-170) REVERT: C 4 HIS cc_start: 0.5153 (OUTLIER) cc_final: 0.4349 (m90) REVERT: C 5 LEU cc_start: 0.5764 (OUTLIER) cc_final: 0.5462 (tt) REVERT: D 5 LEU cc_start: 0.5851 (OUTLIER) cc_final: 0.5531 (tt) REVERT: E 5 LEU cc_start: 0.6083 (OUTLIER) cc_final: 0.5770 (tt) REVERT: F 5 LEU cc_start: 0.6131 (OUTLIER) cc_final: 0.5819 (tt) REVERT: G 5 LEU cc_start: 0.5817 (OUTLIER) cc_final: 0.5434 (tt) REVERT: H 5 LEU cc_start: 0.5816 (OUTLIER) cc_final: 0.5439 (tt) REVERT: I 5 LEU cc_start: 0.5610 (OUTLIER) cc_final: 0.5345 (tt) REVERT: I 6 ARG cc_start: 0.5353 (OUTLIER) cc_final: 0.4725 (ttt180) REVERT: K 5 LEU cc_start: 0.5786 (OUTLIER) cc_final: 0.5544 (tt) REVERT: L 5 LEU cc_start: 0.5784 (OUTLIER) cc_final: 0.5520 (tt) REVERT: M 5 LEU cc_start: 0.5604 (OUTLIER) cc_final: 0.5169 (tt) REVERT: N 5 LEU cc_start: 0.5622 (OUTLIER) cc_final: 0.5185 (tt) REVERT: O 2 HIS cc_start: 0.4818 (OUTLIER) cc_final: 0.4319 (t-170) REVERT: O 4 HIS cc_start: 0.5310 (OUTLIER) cc_final: 0.4239 (t70) REVERT: P 2 HIS cc_start: 0.4637 (OUTLIER) cc_final: 0.4120 (t-170) REVERT: P 4 HIS cc_start: 0.5311 (OUTLIER) cc_final: 0.4274 (t70) REVERT: P 5 LEU cc_start: 0.5726 (OUTLIER) cc_final: 0.5488 (tt) REVERT: Q 5 LEU cc_start: 0.6098 (OUTLIER) cc_final: 0.5721 (tt) REVERT: R 5 LEU cc_start: 0.5745 (OUTLIER) cc_final: 0.5377 (tt) REVERT: U 4 HIS cc_start: 0.4586 (OUTLIER) cc_final: 0.4199 (t70) REVERT: W 5 LEU cc_start: 0.6291 (OUTLIER) cc_final: 0.6063 (tt) REVERT: X 5 LEU cc_start: 0.5936 (OUTLIER) cc_final: 0.5678 (tt) REVERT: a 6 ARG cc_start: 0.5774 (OUTLIER) cc_final: 0.5036 (ttm170) REVERT: c 5 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6429 (tt) REVERT: d 5 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6356 (tt) outliers start: 107 outliers final: 54 residues processed: 107 average time/residue: 0.0270 time to fit residues: 3.5232 Evaluate side-chains 85 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 1 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 2 HIS Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 2 HIS Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 HIS Chi-restraints excluded: chain O residue 4 HIS Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 2 HIS Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 2 HIS Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain a residue 6 ARG Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain c residue 1 LEU Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 1 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 5 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.083522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.067010 restraints weight = 7851.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.068302 restraints weight = 5264.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.069369 restraints weight = 3969.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.070252 restraints weight = 3177.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.070939 restraints weight = 2645.252| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5068 moved from start: 1.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.269 2040 Z= 4.004 Angle : 5.739 34.508 2670 Z= 2.718 Chirality : 0.410 1.332 330 Planarity : 0.050 0.148 300 Dihedral : 11.173 32.555 270 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 278.96 Ramachandran Plot: Outliers : 30.67 % Allowed : 64.67 % Favored : 4.67 % Rotamer: Outliers : 54.29 % Allowed : 13.81 % Favored : 31.90 % Cbeta Deviations : 12.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -10.74 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG O 6 HIS 0.052 0.013 HIS C 4 Details of bonding type rmsd covalent geometry : bond 0.08026 ( 2010) covalent geometry : angle 5.73879 ( 2670) Misc. bond : bond 0.00550 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 0 time to evaluate : 0.048 Fit side-chains REVERT: A 5 LEU cc_start: 0.5767 (OUTLIER) cc_final: 0.5314 (tt) REVERT: B 2 HIS cc_start: 0.5727 (OUTLIER) cc_final: 0.5473 (t-170) REVERT: B 5 LEU cc_start: 0.5755 (OUTLIER) cc_final: 0.5299 (tt) REVERT: C 2 HIS cc_start: 0.5552 (OUTLIER) cc_final: 0.5138 (t-170) REVERT: C 4 HIS cc_start: 0.5444 (OUTLIER) cc_final: 0.4606 (m90) REVERT: C 5 LEU cc_start: 0.5994 (OUTLIER) cc_final: 0.5635 (tt) REVERT: D 5 LEU cc_start: 0.5978 (OUTLIER) cc_final: 0.5725 (tt) REVERT: E 5 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5891 (tt) REVERT: F 5 LEU cc_start: 0.6303 (OUTLIER) cc_final: 0.5973 (tt) REVERT: G 5 LEU cc_start: 0.5941 (OUTLIER) cc_final: 0.5522 (tt) REVERT: H 5 LEU cc_start: 0.5933 (OUTLIER) cc_final: 0.5514 (tt) REVERT: I 5 LEU cc_start: 0.5747 (OUTLIER) cc_final: 0.5507 (tt) REVERT: I 6 ARG cc_start: 0.5490 (OUTLIER) cc_final: 0.4803 (ttt180) REVERT: J 6 ARG cc_start: 0.5582 (OUTLIER) cc_final: 0.4892 (ttt180) REVERT: K 5 LEU cc_start: 0.5896 (OUTLIER) cc_final: 0.5641 (tt) REVERT: L 5 LEU cc_start: 0.5895 (OUTLIER) cc_final: 0.5658 (tt) REVERT: M 4 HIS cc_start: 0.5005 (OUTLIER) cc_final: 0.4026 (t70) REVERT: M 5 LEU cc_start: 0.5747 (OUTLIER) cc_final: 0.5425 (tt) REVERT: N 4 HIS cc_start: 0.5059 (OUTLIER) cc_final: 0.4061 (t70) REVERT: N 5 LEU cc_start: 0.5757 (OUTLIER) cc_final: 0.5426 (tt) REVERT: O 6 ARG cc_start: 0.5528 (OUTLIER) cc_final: 0.4664 (ttm170) REVERT: P 2 HIS cc_start: 0.4884 (OUTLIER) cc_final: 0.4367 (t-170) REVERT: P 4 HIS cc_start: 0.5625 (OUTLIER) cc_final: 0.4603 (t70) REVERT: P 5 LEU cc_start: 0.5930 (OUTLIER) cc_final: 0.5656 (tt) REVERT: Q 5 LEU cc_start: 0.6185 (OUTLIER) cc_final: 0.5791 (tt) REVERT: R 5 LEU cc_start: 0.5868 (OUTLIER) cc_final: 0.5503 (tt) REVERT: U 4 HIS cc_start: 0.4848 (OUTLIER) cc_final: 0.4601 (t70) REVERT: U 6 ARG cc_start: 0.5649 (OUTLIER) cc_final: 0.5156 (ttt180) REVERT: V 6 ARG cc_start: 0.5771 (OUTLIER) cc_final: 0.5341 (ttt180) REVERT: W 5 LEU cc_start: 0.6362 (OUTLIER) cc_final: 0.6117 (tt) REVERT: X 5 LEU cc_start: 0.6076 (OUTLIER) cc_final: 0.5812 (tt) REVERT: a 6 ARG cc_start: 0.5820 (OUTLIER) cc_final: 0.4977 (ttt180) REVERT: b 6 ARG cc_start: 0.5813 (OUTLIER) cc_final: 0.5045 (ttm170) REVERT: c 5 LEU cc_start: 0.6734 (OUTLIER) cc_final: 0.6486 (tt) REVERT: d 5 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6447 (tt) outliers start: 114 outliers final: 57 residues processed: 114 average time/residue: 0.0366 time to fit residues: 4.8243 Evaluate side-chains 93 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 1 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 2 HIS Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 2 HIS Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 6 ARG Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 2 HIS Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 2 HIS Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain V residue 6 ARG Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain a residue 6 ARG Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain c residue 1 LEU Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 1 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 5 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.083625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.066764 restraints weight = 8408.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.068139 restraints weight = 5535.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.069285 restraints weight = 4104.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.069975 restraints weight = 3240.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.070780 restraints weight = 2767.091| |-----------------------------------------------------------------------------| r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5078 moved from start: 1.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.276 2040 Z= 3.995 Angle : 5.748 34.490 2670 Z= 2.728 Chirality : 0.411 1.332 330 Planarity : 0.049 0.145 300 Dihedral : 11.112 32.689 270 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 276.83 Ramachandran Plot: Outliers : 30.67 % Allowed : 64.67 % Favored : 4.67 % Rotamer: Outliers : 52.38 % Allowed : 18.57 % Favored : 29.05 % Cbeta Deviations : 11.90 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.67 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -10.74 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG P 6 HIS 0.052 0.013 HIS C 4 Details of bonding type rmsd covalent geometry : bond 0.08001 ( 2010) covalent geometry : angle 5.74780 ( 2670) Misc. bond : bond 0.00563 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 0 time to evaluate : 0.049 Fit side-chains REVERT: A 5 LEU cc_start: 0.5834 (OUTLIER) cc_final: 0.5410 (tt) REVERT: B 2 HIS cc_start: 0.5714 (OUTLIER) cc_final: 0.5468 (t-170) REVERT: B 5 LEU cc_start: 0.5788 (OUTLIER) cc_final: 0.5324 (tt) REVERT: C 2 HIS cc_start: 0.5634 (OUTLIER) cc_final: 0.5195 (t-170) REVERT: C 4 HIS cc_start: 0.5517 (OUTLIER) cc_final: 0.4669 (m90) REVERT: C 5 LEU cc_start: 0.5964 (OUTLIER) cc_final: 0.5656 (tt) REVERT: D 5 LEU cc_start: 0.6075 (OUTLIER) cc_final: 0.5773 (tt) REVERT: E 5 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5882 (tt) REVERT: F 5 LEU cc_start: 0.6275 (OUTLIER) cc_final: 0.5892 (tt) REVERT: G 5 LEU cc_start: 0.5962 (OUTLIER) cc_final: 0.5541 (tt) REVERT: H 5 LEU cc_start: 0.5939 (OUTLIER) cc_final: 0.5518 (tt) REVERT: I 5 LEU cc_start: 0.5655 (OUTLIER) cc_final: 0.5447 (tt) REVERT: I 6 ARG cc_start: 0.5475 (OUTLIER) cc_final: 0.4822 (ttt180) REVERT: J 6 ARG cc_start: 0.5555 (OUTLIER) cc_final: 0.4751 (ttt180) REVERT: K 5 LEU cc_start: 0.5908 (OUTLIER) cc_final: 0.5660 (tt) REVERT: L 5 LEU cc_start: 0.5891 (OUTLIER) cc_final: 0.5645 (tt) REVERT: M 4 HIS cc_start: 0.5005 (OUTLIER) cc_final: 0.4043 (t70) REVERT: M 5 LEU cc_start: 0.5768 (OUTLIER) cc_final: 0.5448 (tt) REVERT: N 4 HIS cc_start: 0.5085 (OUTLIER) cc_final: 0.4093 (t70) REVERT: N 5 LEU cc_start: 0.5767 (OUTLIER) cc_final: 0.5436 (tt) REVERT: O 6 ARG cc_start: 0.5375 (OUTLIER) cc_final: 0.4556 (ttm170) REVERT: P 2 HIS cc_start: 0.5021 (OUTLIER) cc_final: 0.4575 (t-170) REVERT: P 4 HIS cc_start: 0.5703 (OUTLIER) cc_final: 0.4619 (t70) REVERT: Q 5 LEU cc_start: 0.6152 (OUTLIER) cc_final: 0.5803 (tt) REVERT: R 5 LEU cc_start: 0.5886 (OUTLIER) cc_final: 0.5518 (tt) REVERT: S 6 ARG cc_start: 0.6245 (OUTLIER) cc_final: 0.5969 (ttt-90) REVERT: T 6 ARG cc_start: 0.6267 (OUTLIER) cc_final: 0.5116 (ttm170) REVERT: U 6 ARG cc_start: 0.5678 (OUTLIER) cc_final: 0.4952 (ttm170) REVERT: V 6 ARG cc_start: 0.5735 (OUTLIER) cc_final: 0.5262 (ttt180) REVERT: W 5 LEU cc_start: 0.6276 (OUTLIER) cc_final: 0.5993 (tt) REVERT: X 5 LEU cc_start: 0.6163 (OUTLIER) cc_final: 0.5877 (tt) REVERT: a 6 ARG cc_start: 0.5745 (OUTLIER) cc_final: 0.4923 (ttt180) REVERT: b 6 ARG cc_start: 0.5813 (OUTLIER) cc_final: 0.5040 (ttm170) REVERT: c 5 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6515 (tt) REVERT: d 5 LEU cc_start: 0.6735 (OUTLIER) cc_final: 0.6491 (tt) outliers start: 110 outliers final: 60 residues processed: 110 average time/residue: 0.0493 time to fit residues: 6.1981 Evaluate side-chains 95 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 0 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 2 HIS Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 2 HIS Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 6 ARG Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 2 HIS Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 2 HIS Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain V residue 6 ARG Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain a residue 6 ARG Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain c residue 1 LEU Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 1 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 5 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.083900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.066993 restraints weight = 8532.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.068320 restraints weight = 5593.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.069445 restraints weight = 4175.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.070331 restraints weight = 3301.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.071107 restraints weight = 2724.265| |-----------------------------------------------------------------------------| r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5093 moved from start: 1.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.273 2040 Z= 3.987 Angle : 5.752 34.477 2670 Z= 2.737 Chirality : 0.413 1.333 330 Planarity : 0.049 0.144 300 Dihedral : 11.081 33.356 270 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 277.30 Ramachandran Plot: Outliers : 31.33 % Allowed : 64.00 % Favored : 4.67 % Rotamer: Outliers : 53.33 % Allowed : 16.19 % Favored : 30.48 % Cbeta Deviations : 11.90 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -10.73 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG T 6 HIS 0.052 0.012 HIS C 4 Details of bonding type rmsd covalent geometry : bond 0.07987 ( 2010) covalent geometry : angle 5.75250 ( 2670) Misc. bond : bond 0.00547 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 0 time to evaluate : 0.090 Fit side-chains REVERT: A 5 LEU cc_start: 0.5842 (OUTLIER) cc_final: 0.5418 (tt) REVERT: B 2 HIS cc_start: 0.5731 (OUTLIER) cc_final: 0.5483 (t-170) REVERT: B 5 LEU cc_start: 0.5816 (OUTLIER) cc_final: 0.5349 (tt) REVERT: C 2 HIS cc_start: 0.5563 (OUTLIER) cc_final: 0.5084 (t-170) REVERT: C 4 HIS cc_start: 0.5523 (OUTLIER) cc_final: 0.4686 (m90) REVERT: C 5 LEU cc_start: 0.6199 (OUTLIER) cc_final: 0.5846 (tt) REVERT: D 5 LEU cc_start: 0.5825 (OUTLIER) cc_final: 0.5516 (tt) REVERT: E 5 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.5952 (tt) REVERT: F 5 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.5925 (tt) REVERT: G 5 LEU cc_start: 0.5977 (OUTLIER) cc_final: 0.5554 (tt) REVERT: H 5 LEU cc_start: 0.5962 (OUTLIER) cc_final: 0.5537 (tt) REVERT: I 5 LEU cc_start: 0.5809 (OUTLIER) cc_final: 0.5603 (tt) REVERT: I 6 ARG cc_start: 0.5358 (OUTLIER) cc_final: 0.4804 (ttt180) REVERT: J 6 ARG cc_start: 0.5451 (OUTLIER) cc_final: 0.4658 (ttt180) REVERT: K 5 LEU cc_start: 0.5953 (OUTLIER) cc_final: 0.5718 (tt) REVERT: L 5 LEU cc_start: 0.5944 (OUTLIER) cc_final: 0.5711 (tt) REVERT: M 4 HIS cc_start: 0.5035 (OUTLIER) cc_final: 0.4057 (t70) REVERT: M 5 LEU cc_start: 0.5817 (OUTLIER) cc_final: 0.5510 (tt) REVERT: N 4 HIS cc_start: 0.5121 (OUTLIER) cc_final: 0.4124 (t70) REVERT: N 5 LEU cc_start: 0.5828 (OUTLIER) cc_final: 0.5513 (tt) REVERT: O 2 HIS cc_start: 0.5256 (OUTLIER) cc_final: 0.5039 (t-170) REVERT: P 2 HIS cc_start: 0.4951 (OUTLIER) cc_final: 0.4389 (t-170) REVERT: P 4 HIS cc_start: 0.5619 (OUTLIER) cc_final: 0.4511 (t70) REVERT: Q 5 LEU cc_start: 0.6098 (OUTLIER) cc_final: 0.5760 (tt) REVERT: R 5 LEU cc_start: 0.5950 (OUTLIER) cc_final: 0.5640 (tt) REVERT: S 6 ARG cc_start: 0.6251 (OUTLIER) cc_final: 0.5964 (ttt-90) REVERT: U 6 ARG cc_start: 0.5545 (OUTLIER) cc_final: 0.4914 (ttt180) REVERT: V 6 ARG cc_start: 0.5774 (OUTLIER) cc_final: 0.5297 (ttt180) REVERT: W 5 LEU cc_start: 0.6276 (OUTLIER) cc_final: 0.5980 (tt) REVERT: X 5 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.6151 (tt) REVERT: Z 6 ARG cc_start: 0.6383 (OUTLIER) cc_final: 0.5073 (ttm170) REVERT: a 4 HIS cc_start: 0.5606 (OUTLIER) cc_final: 0.4896 (t70) REVERT: b 6 ARG cc_start: 0.5852 (OUTLIER) cc_final: 0.5105 (ttt180) REVERT: c 5 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6575 (tt) REVERT: d 5 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6557 (tt) outliers start: 112 outliers final: 60 residues processed: 112 average time/residue: 0.0681 time to fit residues: 8.6484 Evaluate side-chains 95 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 0 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain J residue 1 LEU Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 2 HIS Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 2 HIS Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 2 HIS Chi-restraints excluded: chain O residue 6 ARG Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 2 HIS Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain V residue 6 ARG Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain Z residue 6 ARG Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain c residue 1 LEU Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 5 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.084026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.067154 restraints weight = 8218.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.068469 restraints weight = 5445.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.069580 restraints weight = 4080.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.070319 restraints weight = 3241.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.071092 restraints weight = 2762.607| |-----------------------------------------------------------------------------| r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5087 moved from start: 1.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.275 2040 Z= 3.981 Angle : 5.781 34.487 2670 Z= 2.743 Chirality : 0.413 1.340 330 Planarity : 0.049 0.143 300 Dihedral : 11.141 33.589 270 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 276.83 Ramachandran Plot: Outliers : 30.00 % Allowed : 65.33 % Favored : 4.67 % Rotamer: Outliers : 53.33 % Allowed : 17.62 % Favored : 29.05 % Cbeta Deviations : 11.90 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.67 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -10.74 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG T 6 HIS 0.052 0.013 HIS C 4 Details of bonding type rmsd covalent geometry : bond 0.07990 ( 2010) covalent geometry : angle 5.78147 ( 2670) Misc. bond : bond 0.00554 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 0 time to evaluate : 0.088 Fit side-chains REVERT: A 5 LEU cc_start: 0.5836 (OUTLIER) cc_final: 0.5415 (tt) REVERT: B 2 HIS cc_start: 0.5725 (OUTLIER) cc_final: 0.5432 (t-170) REVERT: B 5 LEU cc_start: 0.5813 (OUTLIER) cc_final: 0.5348 (tt) REVERT: C 2 HIS cc_start: 0.5544 (OUTLIER) cc_final: 0.5080 (t-170) REVERT: C 4 HIS cc_start: 0.5516 (OUTLIER) cc_final: 0.4683 (m90) REVERT: C 5 LEU cc_start: 0.6095 (OUTLIER) cc_final: 0.5675 (tt) REVERT: D 2 HIS cc_start: 0.5909 (OUTLIER) cc_final: 0.5667 (t-170) REVERT: D 5 LEU cc_start: 0.5833 (OUTLIER) cc_final: 0.5488 (tt) REVERT: E 2 HIS cc_start: 0.6146 (OUTLIER) cc_final: 0.5937 (t70) REVERT: E 5 LEU cc_start: 0.6300 (OUTLIER) cc_final: 0.5951 (tt) REVERT: F 5 LEU cc_start: 0.6405 (OUTLIER) cc_final: 0.6014 (tt) REVERT: G 5 LEU cc_start: 0.5972 (OUTLIER) cc_final: 0.5550 (tt) REVERT: H 5 LEU cc_start: 0.5961 (OUTLIER) cc_final: 0.5539 (tt) REVERT: I 6 ARG cc_start: 0.5397 (OUTLIER) cc_final: 0.4712 (ttt180) REVERT: J 6 ARG cc_start: 0.5441 (OUTLIER) cc_final: 0.4676 (ttt180) REVERT: K 5 LEU cc_start: 0.5948 (OUTLIER) cc_final: 0.5710 (tt) REVERT: L 5 LEU cc_start: 0.5932 (OUTLIER) cc_final: 0.5698 (tt) REVERT: M 2 HIS cc_start: 0.4316 (OUTLIER) cc_final: 0.3451 (t-170) REVERT: M 4 HIS cc_start: 0.5194 (OUTLIER) cc_final: 0.4117 (t70) REVERT: M 5 LEU cc_start: 0.5810 (OUTLIER) cc_final: 0.5509 (tt) REVERT: N 2 HIS cc_start: 0.4517 (OUTLIER) cc_final: 0.3631 (t-170) REVERT: N 4 HIS cc_start: 0.5284 (OUTLIER) cc_final: 0.4184 (t70) REVERT: N 5 LEU cc_start: 0.5828 (OUTLIER) cc_final: 0.5518 (tt) REVERT: P 6 ARG cc_start: 0.5513 (OUTLIER) cc_final: 0.4750 (ttm170) REVERT: Q 5 LEU cc_start: 0.6134 (OUTLIER) cc_final: 0.5815 (tt) REVERT: R 5 LEU cc_start: 0.5957 (OUTLIER) cc_final: 0.5652 (tt) REVERT: S 6 ARG cc_start: 0.6339 (OUTLIER) cc_final: 0.6121 (ttt-90) REVERT: U 6 ARG cc_start: 0.5584 (OUTLIER) cc_final: 0.4877 (ttt180) REVERT: V 6 ARG cc_start: 0.5737 (OUTLIER) cc_final: 0.5214 (ttt180) REVERT: W 5 LEU cc_start: 0.6301 (OUTLIER) cc_final: 0.5993 (tt) REVERT: X 5 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.6151 (tt) REVERT: Y 6 ARG cc_start: 0.6431 (OUTLIER) cc_final: 0.5089 (ttm170) REVERT: Z 6 ARG cc_start: 0.6386 (OUTLIER) cc_final: 0.5054 (ttm170) REVERT: a 4 HIS cc_start: 0.5628 (OUTLIER) cc_final: 0.4905 (t70) REVERT: a 6 ARG cc_start: 0.5783 (OUTLIER) cc_final: 0.5379 (tmt170) REVERT: b 6 ARG cc_start: 0.5840 (OUTLIER) cc_final: 0.5017 (ttt180) REVERT: c 5 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6692 (tt) REVERT: d 5 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6632 (tt) outliers start: 112 outliers final: 62 residues processed: 112 average time/residue: 0.0717 time to fit residues: 9.0165 Evaluate side-chains 101 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 1 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain E residue 4 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 1 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain J residue 1 LEU Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 2 HIS Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 2 HIS Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 2 HIS Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 2 HIS Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 6 ARG Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain V residue 6 ARG Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Y residue 6 ARG Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain Z residue 6 ARG Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain a residue 6 ARG Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 5 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.084015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.067231 restraints weight = 8070.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.068599 restraints weight = 5375.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.069722 restraints weight = 3996.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.070569 restraints weight = 3170.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.071088 restraints weight = 2653.655| |-----------------------------------------------------------------------------| r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5128 moved from start: 1.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.274 2040 Z= 3.979 Angle : 5.780 34.501 2670 Z= 2.743 Chirality : 0.414 1.334 330 Planarity : 0.049 0.140 300 Dihedral : 11.191 33.913 270 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 277.54 Ramachandran Plot: Outliers : 31.33 % Allowed : 64.00 % Favored : 4.67 % Rotamer: Outliers : 50.48 % Allowed : 20.00 % Favored : 29.52 % Cbeta Deviations : 10.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -10.73 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG A 6 HIS 0.053 0.013 HIS C 4 Details of bonding type rmsd covalent geometry : bond 0.07986 ( 2010) covalent geometry : angle 5.78032 ( 2670) Misc. bond : bond 0.00566 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 0 time to evaluate : 0.087 Fit side-chains REVERT: A 5 LEU cc_start: 0.5802 (OUTLIER) cc_final: 0.5350 (tt) REVERT: B 2 HIS cc_start: 0.5759 (OUTLIER) cc_final: 0.5464 (t-170) REVERT: B 5 LEU cc_start: 0.5846 (OUTLIER) cc_final: 0.5383 (tt) REVERT: C 2 HIS cc_start: 0.5587 (OUTLIER) cc_final: 0.5133 (t-170) REVERT: C 4 HIS cc_start: 0.5566 (OUTLIER) cc_final: 0.4721 (m90) REVERT: C 5 LEU cc_start: 0.6145 (OUTLIER) cc_final: 0.5711 (tt) REVERT: D 2 HIS cc_start: 0.5944 (OUTLIER) cc_final: 0.5673 (t-170) REVERT: D 5 LEU cc_start: 0.5910 (OUTLIER) cc_final: 0.5552 (tt) REVERT: E 2 HIS cc_start: 0.6180 (OUTLIER) cc_final: 0.5963 (t70) REVERT: E 5 LEU cc_start: 0.6330 (OUTLIER) cc_final: 0.5965 (tt) REVERT: F 2 HIS cc_start: 0.6212 (OUTLIER) cc_final: 0.5984 (t70) REVERT: F 5 LEU cc_start: 0.6389 (OUTLIER) cc_final: 0.5968 (tt) REVERT: G 5 LEU cc_start: 0.6009 (OUTLIER) cc_final: 0.5582 (tt) REVERT: H 5 LEU cc_start: 0.5997 (OUTLIER) cc_final: 0.5567 (tt) REVERT: I 6 ARG cc_start: 0.5437 (OUTLIER) cc_final: 0.4723 (ttt180) REVERT: J 6 ARG cc_start: 0.5526 (OUTLIER) cc_final: 0.4744 (ttt180) REVERT: K 5 LEU cc_start: 0.6039 (OUTLIER) cc_final: 0.5788 (tt) REVERT: L 5 LEU cc_start: 0.5976 (OUTLIER) cc_final: 0.5739 (tt) REVERT: M 2 HIS cc_start: 0.4368 (OUTLIER) cc_final: 0.3502 (t-170) REVERT: M 4 HIS cc_start: 0.5093 (OUTLIER) cc_final: 0.4078 (t70) REVERT: M 5 LEU cc_start: 0.5862 (OUTLIER) cc_final: 0.5558 (tt) REVERT: N 2 HIS cc_start: 0.4564 (OUTLIER) cc_final: 0.3677 (t-170) REVERT: N 4 HIS cc_start: 0.5188 (OUTLIER) cc_final: 0.4151 (t70) REVERT: N 5 LEU cc_start: 0.5882 (OUTLIER) cc_final: 0.5565 (tt) REVERT: P 6 ARG cc_start: 0.5505 (OUTLIER) cc_final: 0.4783 (ttm170) REVERT: Q 5 LEU cc_start: 0.6102 (OUTLIER) cc_final: 0.5773 (tt) REVERT: R 5 LEU cc_start: 0.6036 (OUTLIER) cc_final: 0.5705 (tt) REVERT: S 6 ARG cc_start: 0.6291 (OUTLIER) cc_final: 0.6044 (ttt-90) REVERT: U 6 ARG cc_start: 0.5810 (OUTLIER) cc_final: 0.5049 (ttt180) REVERT: V 6 ARG cc_start: 0.5756 (OUTLIER) cc_final: 0.4979 (ttt180) REVERT: W 5 LEU cc_start: 0.6313 (OUTLIER) cc_final: 0.6024 (tt) REVERT: X 5 LEU cc_start: 0.6440 (OUTLIER) cc_final: 0.6165 (tt) REVERT: Y 6 ARG cc_start: 0.6400 (OUTLIER) cc_final: 0.5092 (ttm170) REVERT: Z 6 ARG cc_start: 0.6430 (OUTLIER) cc_final: 0.5086 (ttm170) REVERT: a 4 HIS cc_start: 0.5669 (OUTLIER) cc_final: 0.5048 (t70) REVERT: b 4 HIS cc_start: 0.5704 (OUTLIER) cc_final: 0.4930 (t70) REVERT: c 5 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6781 (tt) REVERT: d 5 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6564 (tt) outliers start: 106 outliers final: 60 residues processed: 106 average time/residue: 0.0686 time to fit residues: 8.2385 Evaluate side-chains 98 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 0 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain E residue 4 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 1 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain J residue 1 LEU Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 2 HIS Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 2 HIS Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 2 HIS Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 2 HIS Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 6 ARG Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain V residue 6 ARG Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Y residue 6 ARG Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain Z residue 6 ARG Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 5 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.084230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.067475 restraints weight = 8110.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.068788 restraints weight = 5379.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.069873 restraints weight = 4039.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.070727 restraints weight = 3222.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.071412 restraints weight = 2697.786| |-----------------------------------------------------------------------------| r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5116 moved from start: 1.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.275 2040 Z= 3.973 Angle : 5.779 34.640 2670 Z= 2.743 Chirality : 0.414 1.339 330 Planarity : 0.049 0.146 300 Dihedral : 11.217 34.432 270 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 278.49 Ramachandran Plot: Outliers : 31.33 % Allowed : 64.00 % Favored : 4.67 % Rotamer: Outliers : 49.52 % Allowed : 20.95 % Favored : 29.52 % Cbeta Deviations : 10.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -10.73 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG T 6 HIS 0.053 0.013 HIS C 4 Details of bonding type rmsd covalent geometry : bond 0.07976 ( 2010) covalent geometry : angle 5.77932 ( 2670) Misc. bond : bond 0.00564 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 0 time to evaluate : 0.096 Fit side-chains REVERT: A 5 LEU cc_start: 0.5792 (OUTLIER) cc_final: 0.5341 (tt) REVERT: B 2 HIS cc_start: 0.5744 (OUTLIER) cc_final: 0.5452 (t-170) REVERT: B 5 LEU cc_start: 0.5833 (OUTLIER) cc_final: 0.5367 (tt) REVERT: C 2 HIS cc_start: 0.5566 (OUTLIER) cc_final: 0.5114 (t-170) REVERT: C 4 HIS cc_start: 0.5541 (OUTLIER) cc_final: 0.4704 (m90) REVERT: C 5 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5692 (tt) REVERT: D 2 HIS cc_start: 0.5938 (OUTLIER) cc_final: 0.5665 (t-170) REVERT: D 5 LEU cc_start: 0.5939 (OUTLIER) cc_final: 0.5585 (tt) REVERT: E 5 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.5958 (tt) REVERT: F 5 LEU cc_start: 0.6381 (OUTLIER) cc_final: 0.5961 (tt) REVERT: G 5 LEU cc_start: 0.5996 (OUTLIER) cc_final: 0.5570 (tt) REVERT: H 5 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5554 (tt) REVERT: I 6 ARG cc_start: 0.5415 (OUTLIER) cc_final: 0.4709 (ttt180) REVERT: J 6 ARG cc_start: 0.5522 (OUTLIER) cc_final: 0.4716 (ttt180) REVERT: K 5 LEU cc_start: 0.6027 (OUTLIER) cc_final: 0.5778 (tt) REVERT: L 5 LEU cc_start: 0.6050 (OUTLIER) cc_final: 0.5835 (tt) REVERT: M 2 HIS cc_start: 0.4347 (OUTLIER) cc_final: 0.3488 (t-170) REVERT: M 4 HIS cc_start: 0.5075 (OUTLIER) cc_final: 0.4060 (t70) REVERT: M 5 LEU cc_start: 0.5856 (OUTLIER) cc_final: 0.5545 (tt) REVERT: N 2 HIS cc_start: 0.4529 (OUTLIER) cc_final: 0.3650 (t-170) REVERT: N 4 HIS cc_start: 0.5162 (OUTLIER) cc_final: 0.4123 (t70) REVERT: N 5 LEU cc_start: 0.5870 (OUTLIER) cc_final: 0.5554 (tt) REVERT: Q 5 LEU cc_start: 0.6140 (OUTLIER) cc_final: 0.5797 (tt) REVERT: R 5 LEU cc_start: 0.6019 (OUTLIER) cc_final: 0.5688 (tt) REVERT: S 6 ARG cc_start: 0.6209 (OUTLIER) cc_final: 0.5976 (ttt-90) REVERT: U 6 ARG cc_start: 0.5795 (OUTLIER) cc_final: 0.5039 (ttt180) REVERT: V 6 ARG cc_start: 0.5822 (OUTLIER) cc_final: 0.5119 (ttt180) REVERT: W 5 LEU cc_start: 0.6306 (OUTLIER) cc_final: 0.6018 (tt) REVERT: X 5 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.6157 (tt) REVERT: Y 6 ARG cc_start: 0.6393 (OUTLIER) cc_final: 0.5085 (ttm170) REVERT: Z 6 ARG cc_start: 0.6419 (OUTLIER) cc_final: 0.5078 (ttm170) REVERT: a 4 HIS cc_start: 0.5650 (OUTLIER) cc_final: 0.5136 (t70) REVERT: b 4 HIS cc_start: 0.5702 (OUTLIER) cc_final: 0.5012 (t70) REVERT: c 5 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6775 (tt) REVERT: d 5 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6554 (tt) outliers start: 104 outliers final: 61 residues processed: 104 average time/residue: 0.0703 time to fit residues: 8.2831 Evaluate side-chains 96 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 0 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 4 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 1 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain J residue 1 LEU Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 2 HIS Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 2 HIS Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 6 ARG Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain V residue 6 ARG Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Y residue 6 ARG Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain Z residue 6 ARG Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 5 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.083079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.067697 restraints weight = 9678.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.068985 restraints weight = 6063.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.070058 restraints weight = 4418.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.070955 restraints weight = 3447.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.071497 restraints weight = 2823.641| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4973 moved from start: 1.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.275 2040 Z= 3.975 Angle : 5.792 34.670 2670 Z= 2.746 Chirality : 0.415 1.342 330 Planarity : 0.049 0.140 300 Dihedral : 11.238 35.799 270 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 278.72 Ramachandran Plot: Outliers : 32.00 % Allowed : 63.33 % Favored : 4.67 % Rotamer: Outliers : 46.19 % Allowed : 23.33 % Favored : 30.48 % Cbeta Deviations : 10.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -10.73 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG T 6 HIS 0.053 0.013 HIS C 4 Details of bonding type rmsd covalent geometry : bond 0.07986 ( 2010) covalent geometry : angle 5.79232 ( 2670) Misc. bond : bond 0.00561 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 280.74 seconds wall clock time: 6 minutes 15.22 seconds (375.22 seconds total)